8SA9

Crystal Structure of Cystathionine beta lyase from Klebsiella aerogenes, PLP-Oxamate Adduct (C2 form)

• PDB DOI: https://doi.org/10.2210/pdb8SA9/pdb

• Classification: LYASE
• Organism(s): Klebsiella aerogenes KCTC 2190
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-03-31 Released: 2023-04-12 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.137 
• R-Value Work: 0.125 
• R-Value Observed: 0.125 

Starting Model: experimental

Literature

Crystal Structure of Cystathionine beta lyase from Klebsiella aerogenes, PLP-Oxamate Adduct (C2 form)

Liu, L., Lovell, S., Battaile, K.P., Cooper, A.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 89.53 kDa 
• Atom Count: 7,378 
• Modelled Residue Count: 786 
• Deposited Residue Count: 806 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cystathionine beta-lyase	A, B	403	Klebsiella aerogenes KCTC 2190	Mutation(s): 2  Gene Names: EAE_03480 EC: 4.4.1.8
UniProt
Find proteins for A0A0H3FMF8 (Klebsiella aerogenes (strain ATCC 13048 / DSM 30053 / CCUG 1429 / JCM 1235 / KCTC 2190 / NBRC 13534 / NCIMB 10102 / NCTC 10006 / CDC 819-56)) Explore A0A0H3FMF8  Go to UniProtKB:  A0A0H3FMF8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZTS (Subject of Investigation/LOI)	C [auth A], F [auth B]	[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino](oxo)acetic acid C10 H13 N2 O8 P UBNNJGPDPGHCQB-UHFFFAOYSA-N
PLP (Subject of Investigation/LOI)	D [auth A], G [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
FLC	E [auth B]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.137 
• R-Value Work: 0.125 
• R-Value Observed: 0.125 
• Space Group: C 1 2 1
• Diffraction Data: https://doi.org/10.18430/M38SA9

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.313	α = 90
b = 131.511	β = 103.81
c = 82.585	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-04-12 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00036
National Institutes of Health/Office of the Director	United States	OD030394

Revision History  

• Version 1.0: 2023-04-12
  Type: Initial release